Fixing validate issues

htseq.wdl

@@ -5,7 +5,8 @@ import "common.wdl"
 task HTSeqCount {
     input {
         String? preCommand
-        Array[IndexedBamFile] inputBamFiles
+        Array[File]+ inputBams
+        Array[File]+ inputBamsIndex
         File gtfFile
         String outputTable
         String format = "bam"
@@ -23,7 +24,7 @@ task HTSeqCount {
         -f ~{format} \
         -r ~{order} \
         -s ~{stranded} \
-        ~{sep=" " inputBamFiles.file} \
+        ~{sep=" " inputBams} \
         ~{gtfFile} \
         > ~{outputTable}
     }

macs2.wdl

@@ -5,7 +5,8 @@ import "common.wdl"
 task PeakCalling {
     input {
         String? preCommand
-        Array[IndexedBamFile] bamFiles
+        Array[File]+ inputBams
+        Array[File]+ inputBamsIndex
         String outDir
         String sampleName
         Int threads = 1
@@ -17,7 +18,7 @@ task PeakCalling {
         set -e -o pipefail
         ~{preCommand}
         macs2 callpeak \
-        --treatment ~{sep = ' ' bamFiles.file} \
+        --treatment ~{sep = ' ' inputBams} \
         --outdir ~{outDir} \
         --name ~{sampleName} \
         ~{true='--nomodel' false='' nomodel}

manta.wdl

@@ -19,11 +19,13 @@ task ConfigureSomatic {
         then installDir + "bin/configMata.py"
         else "configManta.py"
 
+    String normalArg = if (defined(normalBam)) then "--normalBam " + select_first([normalBam]).file else ""
+
     command {
         set -e -o pipefail
         ~{preCommand}
         ~{toolCommand} \
-        ~{"--normalBam " + normalBam.file} \
+        ~{normalArg} \
         ~{"--tumorBam " + tumorBam.file} \
         --referenceFasta ~{reference.fasta} \
         ~{"--callRegions " + callRegions} \

vardict.wdl

@@ -25,6 +25,8 @@ task VarDict {
         Float memoryMultiplier = 2.0
     }
 
+    String normalArg = if (defined(normalBam)) then "|" + select_first([normalBam]).file else ""
+
     String toolCommand = if defined(installDir)
         then installDir + "/VarDict"
         else if useJavaVersion
@@ -38,7 +40,7 @@ task VarDict {
         ~{toolCommand} \
         -G ~{reference.fasta} \
         -N ~{tumorSampleName} \
-        -b "~{tumorBam.file}~{"|" + normalBam.file}" \
+        -b "~{tumorBam.file}~{normalArg}" \
         ~{true="" false="-z" defined(normalBam)} \
         -c ~{chromosomeColumn} \
         -S ~{startColumn} \